Modified atmosphere packaging (MAP) technology offers the possibility to retard the respiration rate and extend the shelf life of fresh produce, and is increasingly used globally as value adding in the fresh and fresh-cut food industry. However, the outbreaks of foodborne diseases and emergence of resistant foodborne pathogens in MAP have heightened public interest on the effects of MAP technology on the survival and growth of pathogenic organisms. This paper critically reviews the effects of MAP on the microbiological safety of fresh or fresh-cut produce, including the role of innovative tools such as the use of pressurised inert/noble gases, predictive microbiology and intelligent packaging in the advancement of MAP safety. The integration of Hazard Analysis and Critical Control Points-based programs to ensure fresh food quality and microbial safety in packaging technology is highlighted.